void colorIsosurface() {
if (params.isSquared && volumeData != null) volumeData.filterData(true, Float.NaN);
/* if (params.isContoured && marchingSquares == null) {
// if (params.isContoured && !(jvxlDataIs2dContour || params.thePlane != null)) {
Logger.error("Isosurface error: Cannot contour this type of data.");
return;
}
*/
if (meshDataServer != null) {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
}
jvxlData.saveVertexCount = 0;
if (params.isContoured && marchingSquares != null) {
initializeMapping();
params.setMapRanges(this, false);
marchingSquares.setMinMax(params.valueMappedToRed, params.valueMappedToBlue);
jvxlData.saveVertexCount = marchingSquares.contourVertexCount;
contourVertexCount =
marchingSquares.generateContourData(
jvxlDataIs2dContour, (params.isSquared ? 1e-8f : 1e-4f));
jvxlData.contourValuesUsed = marchingSquares.getContourValues();
minMax = marchingSquares.getMinMax();
if (meshDataServer != null) meshDataServer.notifySurfaceGenerationCompleted();
finalizeMapping();
}
applyColorScale();
jvxlData.nContours = (params.contourFromZero ? params.nContours : -1 - params.nContours);
jvxlData.jvxlFileMessage =
"mapped: min = " + params.valueMappedToRed + "; max = " + params.valueMappedToBlue;
}
private void colorData() {
float[] vertexValues = meshData.vertexValues;
short[] vertexColixes = meshData.vertexColixes;
meshData.polygonColixes = null;
float valueBlue = jvxlData.valueMappedToBlue;
float valueRed = jvxlData.valueMappedToRed;
short minColorIndex = jvxlData.minColorIndex;
short maxColorIndex = jvxlData.maxColorIndex;
if (params.colorEncoder == null) params.colorEncoder = new ColorEncoder(null);
params.colorEncoder.setRange(
params.valueMappedToRed, params.valueMappedToBlue, params.isColorReversed);
for (int i = meshData.vertexCount; --i >= 0; ) {
float value = vertexValues[i];
if (minColorIndex >= 0) {
if (value <= 0) vertexColixes[i] = minColorIndex;
else if (value > 0) vertexColixes[i] = maxColorIndex;
} else {
if (value <= valueRed) value = valueRed;
if (value >= valueBlue) value = valueBlue;
vertexColixes[i] = params.colorEncoder.getColorIndex(value);
}
}
if ((params.nContours > 0 || jvxlData.contourValues != null)
&& jvxlData.contourColixes == null) {
int n = (jvxlData.contourValues == null ? params.nContours : jvxlData.contourValues.length);
short[] colors = jvxlData.contourColixes = new short[n];
float[] values = jvxlData.contourValues;
if (values == null) values = jvxlData.contourValuesUsed;
if (jvxlData.contourValuesUsed == null)
jvxlData.contourValuesUsed = (values == null ? new float[n] : values);
float dv = (valueBlue - valueRed) / (n + 1);
// n + 1 because we want n lines between n + 1 slices
params.colorEncoder.setRange(
params.valueMappedToRed, params.valueMappedToBlue, params.isColorReversed);
for (int i = 0; i < n; i++) {
float v = (values == null ? valueRed + (i + 1) * dv : values[i]);
jvxlData.contourValuesUsed[i] = v;
colors[i] = Graphics3D.getColixTranslucent(params.colorEncoder.getArgb(v));
}
// TODO -- this strips translucency
jvxlData.contourColors = Graphics3D.getHexCodes(colors);
}
}
void resetIsosurface() {
meshData = new MeshData();
xyzMin = xyzMax = null;
jvxlData.isBicolorMap = params.isBicolorMap;
if (meshDataServer != null) meshDataServer.fillMeshData(null, 0, null);
contourVertexCount = 0;
if (params.cutoff == Float.MAX_VALUE) params.cutoff = defaultCutoff;
jvxlData.jvxlSurfaceData = "";
jvxlData.jvxlEdgeData = "";
jvxlData.jvxlColorData = "";
// TODO: more resets of jvxlData?
edgeCount = 0;
edgeFractionBase = JvxlCoder.defaultEdgeFractionBase;
edgeFractionRange = JvxlCoder.defaultEdgeFractionRange;
colorFractionBase = JvxlCoder.defaultColorFractionBase;
colorFractionRange = JvxlCoder.defaultColorFractionRange;
params.mappedDataMin = Float.MAX_VALUE;
}
private void generateSurfaceData() {
edgeData = "";
if (vertexDataOnly) {
try {
readSurfaceData(false);
} catch (Exception e) {
e.printStackTrace();
Logger.error("Exception in SurfaceReader::readSurfaceData: " + e.getMessage());
}
return;
}
contourVertexCount = 0;
int contourType = -1;
marchingSquares = null;
if (params.thePlane != null || params.isContoured) {
marchingSquares =
new MarchingSquares(
this,
volumeData,
params.thePlane,
params.contoursDiscrete,
params.nContours,
params.thisContour,
params.contourFromZero);
contourType = marchingSquares.getContourType();
marchingSquares.setMinMax(params.valueMappedToRed, params.valueMappedToBlue);
}
params.contourType = contourType;
params.isXLowToHigh = isXLowToHigh;
marchingCubes = new MarchingCubes(this, volumeData, params, jvxlVoxelBitSet);
String data = marchingCubes.getEdgeData();
if (params.thePlane == null) edgeData = data;
jvxlData.setSurfaceInfoFromBitSet(marchingCubes.getBsVoxels(), params.thePlane);
jvxlData.jvxlExcluded = params.bsExcluded;
if (isJvxl) edgeData = jvxlEdgeDataRead;
postProcessVertices();
}
void applyColorScale() {
colorFractionBase = jvxlData.colorFractionBase = JvxlCoder.defaultColorFractionBase;
colorFractionRange = jvxlData.colorFractionRange = JvxlCoder.defaultColorFractionRange;
if (params.colorPhase == 0) params.colorPhase = 1;
if (meshDataServer == null) {
meshData.vertexColixes = new short[meshData.vertexCount];
} else {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
if (params.contactPair == null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_COLOR_INDEXES, null);
}
// colorBySign is true when colorByPhase is true, but not vice-versa
// old: boolean saveColorData = !(params.colorByPhase && !params.isBicolorMap &&
// !params.colorBySign); //sorry!
boolean saveColorData =
(params.colorDensity || params.isBicolorMap || params.colorBySign || !params.colorByPhase);
if (params.contactPair != null) saveColorData = false;
// colors mappable always now
jvxlData.isJvxlPrecisionColor = true;
jvxlData.vertexCount = (contourVertexCount > 0 ? contourVertexCount : meshData.vertexCount);
jvxlData.minColorIndex = -1;
jvxlData.maxColorIndex = 0;
jvxlData.contourValues = params.contoursDiscrete;
jvxlData.isColorReversed = params.isColorReversed;
if (!params.colorDensity)
if (params.isBicolorMap && !params.isContoured || params.colorBySign) {
jvxlData.minColorIndex =
Graphics3D.getColixTranslucent(
Graphics3D.getColix(params.isColorReversed ? params.colorPos : params.colorNeg),
jvxlData.translucency != 0,
jvxlData.translucency);
jvxlData.maxColorIndex =
Graphics3D.getColixTranslucent(
Graphics3D.getColix(params.isColorReversed ? params.colorNeg : params.colorPos),
jvxlData.translucency != 0,
jvxlData.translucency);
}
jvxlData.isTruncated = (jvxlData.minColorIndex >= 0 && !params.isContoured);
boolean useMeshDataValues =
jvxlDataIs2dContour
||
// !jvxlDataIs2dContour && (params.isContoured && jvxlData.jvxlPlane != null ||
hasColorData
|| vertexDataOnly
|| params.colorDensity
|| params.isBicolorMap && !params.isContoured;
if (!useMeshDataValues) {
if (haveSurfaceAtoms && meshData.vertexSource == null)
meshData.vertexSource = new int[meshData.vertexCount];
float min = Float.MAX_VALUE;
float max = -Float.MAX_VALUE;
float value;
initializeMapping();
for (int i = meshData.vertexCount; --i >= meshData.mergeVertexCount0; ) {
/* right, so what we are doing here is setting a range within the
* data for which we want red-->blue, but returning the actual
* number so it can be encoded more precisely. This turned out to be
* the key to making the JVXL contours work.
*
*/
if (params.colorBySets) {
value = meshData.vertexSets[i];
} else if (params.colorByPhase) {
value = getPhase(meshData.vertices[i]);
// else if (jvxlDataIs2dContour)
// marchingSquares
// .getInterpolatedPixelValue(meshData.vertices[i]);
} else {
value = volumeData.lookupInterpolatedVoxelValue(meshData.vertices[i]);
if (haveSurfaceAtoms) meshData.vertexSource[i] = getSurfaceAtomIndex();
}
if (value < min) min = value;
if (value > max && value != Float.MAX_VALUE) max = value;
meshData.vertexValues[i] = value;
}
if (params.rangeSelected && minMax == null) minMax = new float[] {min, max};
finalizeMapping();
}
params.setMapRanges(this, true);
jvxlData.mappedDataMin = params.mappedDataMin;
jvxlData.mappedDataMax = params.mappedDataMax;
jvxlData.valueMappedToRed = params.valueMappedToRed;
jvxlData.valueMappedToBlue = params.valueMappedToBlue;
if (params.contactPair == null) colorData();
JvxlCoder.jvxlCreateColorData(jvxlData, (saveColorData ? meshData.vertexValues : null));
if (haveSurfaceAtoms && meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_VERTICES, null);
if (meshDataServer != null && params.colorBySets)
meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_SETS, null);
}
boolean createIsosurface(boolean justForPlane) {
resetIsosurface();
jvxlData.cutoff = Float.NaN;
if (!readAndSetVolumeParameters(justForPlane)) return false;
if (!justForPlane && !Float.isNaN(params.sigma) && !allowSigma) {
if (params.sigma > 0)
Logger.error("Reader does not support SIGMA option -- using cutoff 1.6");
params.cutoff = 1.6f;
}
// negative sigma just ignores the error message
// and means it was inserted by Jmol as a default option
if (params.sigma < 0) params.sigma = -params.sigma;
nPointsX = voxelCounts[0];
nPointsY = voxelCounts[1];
nPointsZ = voxelCounts[2];
jvxlData.isSlabbable = ((params.dataType & Parameters.IS_SLABBABLE) != 0);
jvxlData.insideOut = params.insideOut;
jvxlData.dataXYReversed = params.dataXYReversed;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.nPointsX = nPointsX;
jvxlData.nPointsY = nPointsY;
jvxlData.nPointsZ = nPointsZ;
jvxlData.jvxlVolumeDataXml = volumeData.xmlData;
jvxlData.voxelVolume = volumeData.voxelVolume;
if (justForPlane) {
// float[][][] voxelDataTemp = volumeData.voxelData;
volumeData.setMappingPlane(params.thePlane);
// volumeData.setDataDistanceToPlane(params.thePlane);
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
params.setMapRanges(this, false);
generateSurfaceData();
volumeData.setMappingPlane(null);
// if (volumeData != null)
// volumeData.voxelData = voxelDataTemp;
} else {
if (!readVolumeData(false)) return false;
generateSurfaceData();
}
if (jvxlFileHeaderBuffer != null) {
String s = jvxlFileHeaderBuffer.toString();
int i = s.indexOf('\n', s.indexOf('\n', s.indexOf('\n') + 1) + 1) + 1;
jvxlData.jvxlFileTitle = s.substring(0, i);
}
if (params.contactPair == null) setBoundingBox();
if (!params.isSilent)
Logger.info("boundbox corners " + Escape.escape(xyzMin) + " " + Escape.escape(xyzMax));
jvxlData.boundingBox = new Point3f[] {xyzMin, xyzMax};
jvxlData.dataMin = dataMin;
jvxlData.dataMax = dataMax;
jvxlData.cutoff = (isJvxl ? jvxlCutoff : params.cutoff);
jvxlData.isCutoffAbsolute = params.isCutoffAbsolute;
jvxlData.pointsPerAngstrom = 1f / volumeData.volumetricVectorLengths[0];
jvxlData.jvxlColorData = "";
jvxlData.jvxlPlane = params.thePlane;
jvxlData.jvxlEdgeData = edgeData;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.isContoured = params.isContoured;
jvxlData.colorDensity = params.colorDensity;
if (jvxlData.vContours != null) params.nContours = jvxlData.vContours.length;
jvxlData.nContours = (params.contourFromZero ? params.nContours : -1 - params.nContours);
jvxlData.nEdges = edgeCount;
jvxlData.edgeFractionBase = edgeFractionBase;
jvxlData.edgeFractionRange = edgeFractionRange;
jvxlData.colorFractionBase = colorFractionBase;
jvxlData.colorFractionRange = colorFractionRange;
jvxlData.jvxlDataIs2dContour = jvxlDataIs2dContour;
jvxlData.jvxlDataIsColorMapped = jvxlDataIsColorMapped;
jvxlData.jvxlDataIsColorDensity = jvxlDataIsColorDensity;
jvxlData.isXLowToHigh = isXLowToHigh;
jvxlData.vertexDataOnly = vertexDataOnly;
jvxlData.saveVertexCount = 0;
if (jvxlDataIsColorMapped || jvxlData.nVertexColors > 0) {
if (meshDataServer != null) {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_COLOR_INDEXES, null);
}
jvxlData.jvxlColorData = readColorData();
updateSurfaceData();
if (meshDataServer != null) meshDataServer.notifySurfaceMappingCompleted();
}
return true;
}
void jvxlUpdateInfo() {
jvxlData.jvxlUpdateInfo(params.title, nBytes);
}